Secondary chromosome

Discovery Early in the era of bacterial genomics, the genomes of bacteria were thought to have a relatively simple architecture. All known bacteria had circular chromosomes containing all the crucial genes. Some bacteria had additional replicons known as plasmids, and plasmids were characteristically small, circular, and dispensable (meaning that they only encoded non-essential genes). As more bacteria and their genomes were studied, many alternative forms of bacterial genomic architecture began to be discovered. Linear chromosomes and linear plasmids were discovered in a number of species. Soon after, bacteria with several large replicons were discovered, leading to the view that bacteria, just like eukaryotes, can have a genome made up of more than one chromosome. Burkholderia cepacia complex in 1994, Rhizobium meliloti in 1995, Bacillus thuringiensis in 1996, and now about 10% of bacterial species are known to have large replicons that are separate from the main chromosome. Definition With the onset of these discoveries, several approaches in classifying different components of multipartite genomes were proposed. Various terms have been used to describe large replicons other than the main chromosome, including simply designating them as additional chromosomes, or "minichromosomes", "megaplasmids", or "secondary chromosomes". Criteria used to distinguish between these replicons typically revolve around features such as size and the presence of core genes. The original definition of a 'chromid' involves meeting three criteria: Additional proposed classifications Beyond classifying certain replicons as chromids, a number of scientists have proposed further distinguishing between different types of chromids. One classification distinguishes between primary and secondary chromids. Primary chromids are defined as chromids containing core genes that are always essential for the survival of the bacterium under all conditions. Secondary chromids are defined as chromids essential for survival in the native conditions of the bacterium, but may be non-essential in certain "safe" conditions such as a laboratory environment. Secondary chromids may also have more recent evolutionary origins and may retain some more plasmid-like features as compared with primary chromids. An example of a proposed primary chromid is "chromosome II" of Paracoccus denitrificans PD1222. == Characteristics ==

Size and copy number In a bacterial genome, the main chromosome will always be the largest replicon, followed by the chromid and then the plasmid. One exception to this trend is known in Deinococcus deserti VCD115, where both plasmids are larger than the chromid. While the presence of core genes may lead to the classification of this replicon as a chromid, this replicon may also be excluded on certain definitions. Some approaches only categorize certain replicons as chromids if they meet a threshold size of 350kb. It has also been observed that chromids tend to have a low copy number in the cell, as with chromosomes and megaplasmids. On average, chromids are twice as large as megaplasmids (and so the emergence of a chromid from a megaplasmid is associated with a sizable gene accumulation in the aftermath of the conversion). Genomic features Chromids more frequently have a lower G + C content compared with the main chromosome, although the strength of this association is not very strong. A chromid will also typically have a G + C content within 1% of that of the main chromosome, reflecting its nearing the base composition equilibrium of the main chromosome after having stably existed within a bacterial lineage for a necessary period of time. Chromids also resemble the main chromosome in their codon usage bias. One analysis found that chromids had a median 0.34% difference in GC content with the main chromosome, compared with values of 1.9% for megaplasmids and 2.8% for plasmids. While most chromids have a disproportionately smaller number of essential genes compared to the main chromosome, such as rRNA genes or the genes in the rRNA operon, some may have many more essential genes and may even be considered "equal partners" with the chromosome. In general, chromids also see an enrichment of genes involved in the processes of transport, metabolism, transcription, regulatory functions, signal transduction, and motility-related functions. Proteins located on chromids are involved in processes which can interact with proteins encoded on the main chromosome. Chromids also have more transposase genes than chromosomes, but less than megaplasmids. Due to their stable presence within a bacterial genus, chromids also have a feature of being phylogenetically restricted to specific genera. Examples of genera of bacteria with chromids include Deinococcus, Leptospira, Cyanothece (a type of cyanobacteria), and an enrichment of genera of the Pseudomonadota. Overall, bacterial genome sequencing indicates that roughly 10% of bacterial species have a chromid. chromids do and only replicate once per cell cycle. In the bacterial genus Vibrio, replication of the main chromosome begins before replication of the chromid. The chromid is smaller than the chromosome, and so takes a shorter amount of time to finish replication. For this reason, replication of the chromid is delayed to coordinate replication termination between the chromosome and chromid. Earlier replication of the chromosome compared with the chromid has also been observed in Ensifer meliloti. Bacteria also rely on different replication factors to start replication between the chromosome and the chromid. Replication of the chromosome is initiated upon stimulation of the expression of the protein DnaA, whereas expression of chromid replication requires DnaA but also depends on RctB. This is similar to F1 and P plasmids which also depend on DnaA but still have their replication controlled by other proteins (specifically RepA and RepE). Segregation of the chromid follows different patterns between different genera of bacteria, although it typically takes place after the segregation of the main chromosome. Genes located on chromids are also more prone to evolve and display less purifying selection. Since common species definition for prokaryotes are based on DNA sequence or average nucleotide identity, the greater evolvability of the chromid may result in organisms with chromids having a greater tendency to speciate. == Origins ==

"Schism" and "plasmid" hypotheses Several suggestions have been put forwards to explain the origins of chromids. The two main hypotheses are the "schism hypothesis" and the "plasmid hypothesis". According to the schism hypothesis, two separate bacterial chromosomes may arise through the splitting of one larger chromosome, resulting in a main and a secondary chromosome (or a chromid). However, due to the plasmid-type maintenance and replication systems in chromids as well as the uneven distribution of core genes between the main chromosome and the chromid, the plasmid hypothesis suggesting that chromids evolved from megaplasmids which acquired core genes is widely accepted.'' == References ==